if ("Undetermined".equals(htsfSample.getBarcode())) { continue; SequencerRun sequencerRun = htsfSample.getSequencerRun(); logger.debug("sequencerRun: {}", sequencerRun.toString()); List<File> readPairList = WorkflowUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex()); logger.debug("readPairList.size(): {}", readPairList.size()); File casavaWorkflowDirectory = new File(sequencerRunOutputDirectory, "CASAVA/" + htsfSample.getName()); + htsfSample.getName()); String laneStr = String.format("L%03d", htsfSample.getLaneIndex());
if ("Undetermined".equals(htsfSample.getBarcode())) { continue; logger.info("htsfSample: {}", htsfSample.toString()); String oldSampleName = htsfSample.getName(); SequencerRun sequencerRun = htsfSample.getSequencerRun(); String newSampleName = String.format("L%03d_%s", htsfSample.getLaneIndex(), htsfSample.getBarcode()); logger.info("newSampleName: {}", newSampleName); List<File> readPairList = WorkflowUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex()); String laneStr = String.format("L%03d", htsfSample.getLaneIndex()); htsfSample.setName(newSampleName); Set<EntityAttribute> entityAttributeSet = htsfSample.getAttributes(); for (EntityAttribute entityAttribute : entityAttributeSet) { if (entityAttribute.getName().equals("identity_confirmed")) { Set<FileData> fileDataSet = htsfSample.getFileDatas(); for (FileData fileData : fileDataSet) { String path = fileData.getPath();
sample.getLaneIndex())); File baseCallStatsDir = new File(unalignedDir, String.format("Basecall_Stats_%s", flowcell)); File statsFile = new File(baseCallStatsDir, "Demultiplex_Stats.htm"); Element meanQualityScorePassingFilteringElement = tdIter.next(); if (sample.getName().equals(sampleIdElement.text()) && sample.getLaneIndex().toString().equals(laneElement.text()) && sample.getBarcode().equals(indexElement.text())) { Set<EntityAttribute> attributeSet = sample.getAttributes(); sample.setAttributes(attributeSet); mapseqDAOBean.getHTSFSampleDAO().save(sample); System.out.println(String.format("Successfully saved sample: %s", sample.getId())); logger.info(sample.toString());
if ("Undetermined".equals(htsfSample.getBarcode())) { continue; SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName(), getVersion());
File htsfSampleOutputDir = new File(workflowDir, htsfSample.getName()); File tmpDir = new File(htsfSampleOutputDir, "tmp"); tmpDir.mkdirs(); htsfSample.setOutputDirectory(htsfSampleOutputDir.getAbsolutePath()); getPipelineBeanService().getMaPSeqDAOBean().getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e1) {
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = new File(workflowDir, htsfSample.getName()); File tmpDir = new File(outputDirectory, "tmp"); if (!tmpDir.exists()) { List<File> readPairList = WorkflowUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex()); int idx = htsfSample.getName().lastIndexOf("-"); String participantId = idx != -1 ? htsfSample.getName().substring(0, idx) : htsfSample.getName(); System.out.println("FINISHED PROCESSING: " + htsfSample.toString());
if (laneMap.containsKey(htsfSample.getLaneIndex()) || "Undetermined".equals(htsfSample.getBarcode())) { continue; laneMap.put(htsfSample.getLaneIndex(), new ArrayList<HTSFSample>()); if ("Undetermined".equals(htsfSample.getBarcode())) { continue; laneMap.get(htsfSample.getLaneIndex()).add(htsfSample); SequencerRun sequencerRun = htsfSample.getSequencerRun(); File casavaOutputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, "CASAVA", getVersion()); File projectDirectory = new File(unalignedDir, "Project_" + htsfSample.getStudy().getName()); File sampleDirectory = new File(projectDirectory, "Sample_" + htsfSample.getName()); copy1Job.setSiteName(siteName); File source1File = new File(sampleDirectory, String.format("%s_%s_L%03d_R%d_001.fastq.gz", htsfSample.getName(), htsfSample.getBarcode(), laneIndex, 1)); copy1Job.addArgument(CopyCLI.SOURCE, source1File.getAbsolutePath()); File r1FastqFile = new File(casavaOutputDirectory, String.format("%s_%s_L%03d_R%d.fastq.gz", sequencerRun.getName(), htsfSample.getBarcode(), laneIndex, 1)); copy1Job.addArgument(CopyCLI.DESTINATION, r1FastqFile.getAbsolutePath()); copy1Job.addArgument(CopyCLI.MIMETYPE, MimeType.FASTQ.toString()); copy2Job.setSiteName(siteName); File source2File = new File(sampleDirectory, String.format("%s_%s_L%03d_R%d_001.fastq.gz", htsfSample.getName(), htsfSample.getBarcode(), laneIndex, 2));
if ("Undetermined".equals(htsfSample.getBarcode())) { continue; SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("DOC", ""), getVersion()); Set<EntityAttribute> attributeSet = htsfSample.getAttributes(); if (attributeSet == null) { attributeSet = new HashSet<EntityAttribute>(); Set<FileData> fileDataSet = htsfSample.getFileDatas(); htsfSample.setAttributes(attributeSet); getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) {
if ("Undetermined".equals(htsfSample.getBarcode())) { continue; File outputDirectory = new File(htsfSample.getOutputDirectory()); File tmpDir = new File(outputDirectory, "tmp"); if (!tmpDir.exists()) { Set<FileData> fileDataSet = htsfSample.getFileDatas(); File bamFile = null; int idx = htsfSample.getName().lastIndexOf("-"); String participantId = idx != -1 ? htsfSample.getName().substring(0, idx) : htsfSample.getName();
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName().replace("DOC", ""), getVersion()); Set<FileData> fileDataSet = htsfSample.getFileDatas(); logger.warn("bam file to process was not found: {}", htsfSample.toString()); throw new WorkflowException("bam file to process was not found"); logger.warn("bam index file to process was not found: {}", htsfSample.toString()); throw new WorkflowException("bam index file to process was not found");
SequencerRun sequencerRun = htsfSample.getSequencerRun(); File sequencerRunOutputDirectory = new File(baseDir, sequencerRun.getName()); File workflowDir = new File(sequencerRunOutputDirectory, "NCGenes"); File outputDirectory = new File(workflowDir, htsfSample.getName()); Set<EntityAttribute> attributeSet = htsfSample.getAttributes(); if (attributeSet == null) { attributeSet = new HashSet<EntityAttribute>(); htsfSample.setAttributes(attributeSet); this.mapseqDAOBean.getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) {
if ("Undetermined".equals(htsfSample.getBarcode())) {continue;} SequencerRun sequencerRun = htsfSample.getSequencerRun(); logger.debug("sequencerRun: {}", sequencerRun.toString()); Integer laneIndex = htsfSample.getLaneIndex(); logger.debug("laneIndex = {}", laneIndex);
File outputDirectory = new File(htsfSample.getOutputDirectory()); Set<FileData> fileDataSet = htsfSample.getFileDatas(); logger.warn("vcf file to process was not found: {}", htsfSample.toString()); return; Set<EntityAttribute> attributeSet = htsfSample.getAttributes(); htsfSample.setAttributes(attributeSet); getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) {
if ("Undetermined".equals(htsfSample.getBarcode())) { continue; htsfSampleNameSet.add(htsfSample.getName()); SequencerRun sequencerRun = htsfSampleSet.iterator().next().getSequencerRun();
.toLowerCase()); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPID, String.format("%s-%s_L%03d", sequencerRun.getName(), htsfSample.getBarcode(), htsfSample.getLaneIndex())); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, htsfSample.getBarcode()); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, String.format("L%03d_%s", htsfSample.getLaneIndex(), htsfSample.getBarcode())); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, String.format("L%03d_%s", htsfSample.getLaneIndex(), htsfSample.getBarcode())); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPCENTERNAME, "UNC");
if (!laneClusterDensityTotalMap.containsKey(sample.getLaneIndex())) { laneClusterDensityTotalMap.put(sample.getLaneIndex(), new ArrayList<Double>()); List<Double> laneClusterDensityTotalList = laneClusterDensityTotalMap.get(sample.getLaneIndex()); long clusterDensityTotal = 0; for (Double clusterDensity : laneClusterDensityTotalList) { logger.info("value = {}", value); Set<EntityAttribute> attributeSet = sample.getAttributes(); sample.setAttributes(attributeSet); mapseqDAOBean.getHTSFSampleDAO().save(sample);
job.addArgument("--sequencerRunId", sequencerRun.getId().toString()); } else if (sequencerRun == null && htsfSample != null) { logger.debug("htsfSample.getSequencerRun().getId().toString(): {}", htsfSample.getSequencerRun() .getId().toString()); job.addArgument("--sequencerRunId", htsfSample.getSequencerRun().getId().toString()); logger.debug("htsfSample.getId().toString(): {}", htsfSample.getId().toString()); job.addArgument("--htsfSampleId", htsfSample.getId().toString());
Set<EntityAttribute> attributeSet = htsfSample.getAttributes(); htsfSample.setAttributes(attributeSet); try { mapseqDAOBean.getHTSFSampleDAO().save(htsfSample); logger.debug("Found HTSFSample: {}", htsfSample.toString()); return htsfSample;
sb.append(String.format("HTSFSample Name: %s%n", sample.getName()));
@Override public void postRun() throws WorkflowException { logger.info("ENTERING postRun()"); Set<HTSFSample> htsfSampleSet = getAggregateHTSFSampleSet(); logger.info("htsfSampleSet.size(): {}", htsfSampleSet.size()); for (HTSFSample htsfSample : htsfSampleSet) { SaveBestMatchAttributeRunnable runnable = new SaveBestMatchAttributeRunnable(); runnable.setMapseqDAOBean(getWorkflowBeanService().getMaPSeqDAOBean()); runnable.setHtsfSampleId(htsfSample.getId()); Executors.newSingleThreadExecutor().execute(runnable); } }